Analyses of Genome-Wide Recombination in Sulfolobus islandicus

Recombination is a fundamental process that both maintains genome integrity and dramatically shapes evolutionary dynamics in populations from all domains of life. Here we cross two genetically distinct but highly syntenic sympatric strains of Sulfolobus (Saccharolobus) islandicus and identify the pattern of recombination across the archaeal chromosome. We quantify recombination breakpoints occurring at neutral chromosomal markers through high-throughput short read Illumina sequencing of selected recombinant strains. We focus on three datasets that provide different, but corroborating information: i) individual colony sequences, ii) large colony pools of strains sorted by background genotype, and iii) a large colony pool of combined background genotypes. For each dataset we apply a newly designed and optimized computational tool called MARBL (Multiply Anchored Recombination Breakpoint Locator) for quantifying breakpoints and testing their statistical significance relative to sources of error introduced by sequencing technology. By combining the results of each dataset, we determine the short tract recombination preference in this organism and discuss its implications for mechanisms of recombination in archaea. We demonstrate uniform rates of recombination throughout the chromosome, which differ from previous studies of natural variation and discuss this in light of previous data suggesting speciation occurs through selection against inter-species hybrids. Importance StatementRecombination is a critical process in all domains of life that facilitates the essential repair of chromosomes and exchanges variation between organisms. Here we investigate genome-wide patterns of recombination in the model archaeaon Saccharolobus islandicus to better understand mechanistic aspects of their DNA exchange and recombination processes. Our observations of recombination in a controlled laboratory setting identified patterns of recombination that support the ability to incorporate short pieces of DNA in a piecemeal fashion from larger transferred segments. By comparing these observations to inferred recombination from natural populations, we can gain insight into evolutionary parameters including natural selection that would be otherwise difficult to determine from genomic evidence alone.